The numerous existing primary care-based research networks currently use various data collection methods. In this paper, we compared routine data extracted from general practitioners' (GPs') electronic patient records (EPRs) and GPs' answers to an electronic questionnaire. We investigated for 10,307 Belgian patients 10 healthcare conditions using clinical and biological parameters (cholesterol, blood pressure, and body mass index), diagnoses (hypertension, diabetes, and personal past cardiovascular event(s)), and drug prescriptions (antidiabetic drugs, aspirin, statins, and antihypertensive drugs). We found a relatively fair agreement (Kappa≥0.40) between the two data collection methods for 7 healthcare conditions, but no agreement for the biological parameters. When EPR data was used and compared with the questioning method, the prevalence of diagnoses and drug prescriptions was relatively lower and the prevalence of clinical and biological parameters was relatively higher (all missing data excluded) in the EPR data than in the data collected using the questioning method. Using EPR data, we calculated an acceptable proxy for the prevalence as observed using the questioning method. The comparison of the two data collection methods was a worthwhile approach, in that it could highlight potential ways to improve both care quality and information systems.